MolNFT v1 · #12478 · protein
Structure of the adpr-ase in complex with ampcpr and mg
1KHZ · ADP-ribose pyrophosphatase: “Structure of the adpr-ase in complex with ampcpr and mg”. X-ray diffraction, 3 ligands (ADV, MG, CL), 4 pockets (best druggability 0.75). MolNFT v1 #12478 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KHZ
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose pyrophosphatase
- EC
- 3.6.1.13
- UniProt
- Q93K97
- Ligands
- ADV, MG, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 205 | 27% helix, 38% strand | Q93K97 |
| B | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 202 | 27% helix, 40% strand | Q93K97 |
Ligands and binding sites
- ADV · Alpha-beta methylene adp-ribose · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.75 | 0.85 | 45 | MG, ADV |
| 2 | 303 | 0.68 | 0.83 | 46 | empty |
| 3 | 58 | 0.45 | 0.84 | 16 | empty |
| 4 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3696 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q93K97
- Elsewhere: RCSB PDB 1KHZ · PDBe 1KHZ · UniProt Q93K97
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